With all my experience with minecraft servers I would say the issues you're having with lag are that your host is not providing enough recourse's for the server to run properly, With the amount of people generating new chunks, new builds, automation and much more your host cannot handle it, I suggest either a new host or upgrading add more ram or get be on a dedicated server with a better processor.

Foxy I have been communicating with support. We are using over 60% of the CPU for the whole node and causing lag for their other clients due to our server being very resource hungry. A normal busy server only uses 10% CPU power.

Let me remind you that these boxes are running dual Xeon CPUs and we have 4G of ram to use..

Bez, the server may have a dual xeon CPU and everything you want, but the CPU usuage remains shared , and like everything that's shared, the more people which run a server in the same box your server is hosted at, the less you have available. The same happens with a VPS Server, it will never be as stable as hosting it in a dedicated server, that's a fact.

Running the server Vanilla was a success, the lag has gone and we have pinpointed it to a plugin issue. We are now at a very low CPU usage. I will be redownloading clean plugin .jars and adding plugins back to the server slowly.

I will only add the essential plugins so that we can keep the server running normally.